Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization.

ABSTRACT:

Background

Affymetrix microarray technology allows one to investigate expression of thousands of genes simultaneously upon a variety of conditions. In a popular U133A microarray platform, the expression of 37% of genes is measured by more than one probeset. The discordant expression observed for two different probesets that match the same gene is a widespread phenomenon which is usually underestimated, ignored or disregarded.

Results

Here we evaluate the prevalence of discordant expression in data collected using Affymetrix HG-U133A microarray platform. In U133A, about 30% of genes annotated by two different probesets demonstrate a substantial correlation between independently measured expression values. To our surprise, sorting the probesets according to the nature of the d

SUBMITTER: Marakhonov A 

PROVIDER: S-EPMC4303952 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature